Chapter 6. Nitrogen compounds

Table of Contents

6.1. Nitrogen fixation
6.2. Nitrification
6.3. Denitrification
6.4. Nitrogen deposition
6.5. Anthropogenic sources of nitrogen compounds
6.6 Atmospheric reactions of nitrogen species

Nitrogen is the main constituent of the Earth's atmosphere. Molecular nitrogen (N2) is a colorless odorless gas, with an atmospheric abundance of 78% (Figure 6.1). Nitrogen compounds play an important role in atmospheric chemistry, and some chemical forms are potent greenhouse gases.

Chemical structure of nitrogen molecule

Figure 6.1: Chemical structure of nitrogen molecule

Besides carbon, hydrogen and oxygen, nitrogen is among the most important elements for the biosphere. It can be found in proteins, nucleic acids, vitamins, enzymes and other organic compounds.

Schematic representation of the nitrogen cycle.

Figure 6.2: Schematic representation of the nitrogen cycle. Source: Wikipedia

However, N2 is relatively inert, therefore plants and animals are not capable of assimilating atmospheric nitrogen directly, it has to be transformed to chemical forms consumable for living organisms. Nitrogen nutrient limitation therefore frequently occurs in case of various ecosystems making the nitrogen cycle one of the most studied nutrient cycle in ecology.

The atmospheric N cycle includes three basic processes: nitrogen fixation, gaseous nitrogen emission and deposition of nitrogen compounds (Figure 6.2). Some long lived nitrogen compounds have stratospheric sink as well.

6.1. Nitrogen fixation

Nitrogen fixation is the chemical process that transforms N2 to other nitrogen species that are consumable for living organisms. Plants are able to take up nitrogen in reduced form of ammonia (NH3, Figure 6.3), nitrates (NO3). Two natural ways of nitrogen fixation exist: atmospheric and biological nitrogen fixation.

Chemical structure of ammonia.

Figure 6.3: Chemical structure of ammonia.

(i) Atmospheric nitrogen fixation. First, the dissociation of N2 molecule is required to allow N to combine with other elements. However, N2 being a stable chemical form, the dissociation is a highly energetic process. Therefore N fixation occurs when considerable amount of energy is provided e.g. by lightning. In the subsequent reaction, N combines with atmospheric O or H atoms to form nitric oxides (NO, Figure 6.4) or ammonia (NH3). These species can reach the land surface via wet deposition with rain.

Chemical structure of nitrogen oxide.

Figure 6.4: Chemical structure of nitrogen oxide.

(ii) Biological N fixation BNF: Diazotrophs are organisms in the soil that do not need fixed nitrogen, but they fix nitrogen in their metabolism. There are two types of diazotrophs: symbiotic and free living (non-symbiotic) diazotrophs. A part of plants are supplied with consumable nitrogen nutrition by root symbionts such as legumes or nodule forming bacteria (Rhizobia). Rhizobia (Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium) are very well studied plant symbionts.

Majority of nitrogen fixation happens via biological processes: Rhizobia require inorganic nutrients for their metabolism in which N2 is converted to ammonia by the nitrogenase enzyme:

N2 + 8 H+ + 8 e → 2 NH3 + H2


The legume family (Fabaceae) are important in nitrogen fixation as they are well known to associate with symbiotic rhizobia (Figure 6.5, Figure 6.6, Figure 6.7). These plants are produced agriculturally (beans, peas, etc.) but also occur in natural ecosystems (e.g. white clover).

Rhizobia nodules on cowpea, pea and soybean roots

Figure 6.5: Rhizobia nodules on cowpea, pea and soybean roots. Source: Wikipedia

Rhizobia nodules on pea roots

Figure 6.6 Rhizobia nodules on pea roots. Photo credit László Ködöböcz.

Rhizobia nodules on soybean roots

Figure 6.7 Rhizobia nodules on soybean roots. Photo credit László Ködöböcz.

Free living nitrogen fixing organisms are also present in soils, supplying plants with reduced form of nitrogen. Many bacteria, fungi are capable of producing the nitrogenase enzyme. Cyanobacteria is one of the free living nitrogen fixing bacteria, but note that cyanobacteria also has symbiotic form.

Role of micorhizza in nitrogen fixation Abuscular micorhizza is another root symbiont; these fungi help plants to take up nutrients from the soil. It is associated with the majority of terrestrial plants, and probably played important role in the colonization of the land surface by plants.